...moved to dalaxy-dev, since it is about your local Galaxy instances:
Hi Philippe
Your galaxy wrapper for MACS expects version 1.3, where the option
"--lambdaset" is present. (see
https://github.com/taoliu/MACS/blob/macs_v1/ChangeLog)
Regards, Hans-Rudolf
Original Message --
Hi Jim
If using a standalone server, Galaxy is using its own queuing system,
which you can modify by changing (in universe_wsgi.ini):
local_job_queue_workers
user_job_limit
but the system is not aware of the memory size and number of cores. In
your "specific example", running out of memory i
On 10/29/2012 11:33 AM, James Vincent wrote:
Thanks very much. Sorry for the double post - my first was rejected
due to wroneg email, but I guess it made it through.
Do you happen to know if one can query the number of jobs queued and
running? I'd like to put status monitor somewhere for regul
> Whatever the file type I set for the gff file (gff3, gff or gtf), I get the
> transcript_id error:
>
> Traceback (most recent call last):
> File
> "/home/pgtgal/galaxy-dist/lib/galaxy/datatypes/converters/interval_to_fli.py",
> line 91, in
>main()
> File
> "/home/pgtgal/galaxy-dist/lib
Hello all,
I've written a MrBayes wrapper that accepts a Nexus file (presumably containing
a data block and a command block). In order to make it a bit easier for new
users, I was hoping to be able to let users specify some parameters, such as
their model, in Galaxy, as opposed to including
Ann,
I think you may be able to do this by generating another nexus file
using "configfiles" in the Galaxy tool config which just contains a
command block, similar to the example here:
http://mrbayes.sourceforge.net/wiki/index.php/FAQ#How_do_I_run_MrBayes_in_batch_mode.3F
-- jt
On Mon, Oct
This is a bug that is fixed in revision ecd131b. Sorry for the inconvenience.
-- jt
On Sat, Oct 27, 2012 at 6:12 PM, Luciano Cosme wrote:
> Howdy,
>I installed galaxy in a new server that I build and I am getting the
> following error when I try to upload the files from a local directory.
>
Brilliant, thanks! I had seen the FAQ, but didn't know about configfiles. Much
appreciated!
Ann
-Original Message-
From: ja...@taylorlab.org [mailto:ja...@taylorlab.org] On Behalf Of James Taylor
Sent: Monday, October 29, 2012 2:03 PM
To: Gomez, Ann
Cc: galaxy-dev@lists.bx.psu.edu
Subj
Ann,
Also to your request "I'd appreciate any input about MrBayes or a
similar kind of tool."
We are developing a suite of tools for phylogenetics in Galaxy. We are
calling the tool suite Osiris.
We are currently adding the full tool suite to Bit Bucket:
https://bitbucket.org/repo/all?na
Hi Ann,
Configfiles is the way to go. I have writtent the BEAST (and TreeAnnotator),
Garli, and RAxML wrappers that are all available in the Galaxy ToolShed. BEAST
uses an input xml file that it can parse to execute the analysis. Garli can
take a config file that's generated by the Galaxy from
On Oct 29, 2012, at 3:20 PM, Todd Oakley wrote:
> Ann,
> Also to your request "I'd appreciate any input about MrBayes or a similar
> kind of tool."
>
> We are developing a suite of tools for phylogenetics in Galaxy. We are
> calling the tool suite Osiris.
>
> We are currently adding the
On Oct 29, 2012, at 4:40 PM, Oleksandr Moskalenko wrote:
> This is an interesting project. I'm glad to see more people working on
> phylogenetics related wrappers and workflows. I wonder if we could get a
> "Phylogenetics" category added to the main Galaxy Toolshed, so we could put
> all the r
Hi Alex, Todd; thanks for the info and links! The Garli tool looks a lot more
sophisticated than what I have so far, so I'm sure it will be helpful to look
at.
Ann
-Original Message-
From: Oleksandr Moskalenko [mailto:o...@hpc.ufl.edu]
Sent: Monday, October 29, 2012 4:26 PM
To: Gome
Hi Greg,
> We had some occasions where we'd try to install a tool from the
> toolshed, and it would hang - it appeared that the hg pull was timing
> out.
>
> Was the timeout a regular occurrence? if so, do you know that cause, and
> were you able to get it resolved?
>
It was repeated, but after a
Hi all,
We are looking at wrapping trimmomatic (
http://www.usadellab.org/cms/index.php?page=trimmomatic ). However to
run, it requires the Illumina adaptor sequences, which are copyright.
I was wondering if anyone has already dealt with this issue when
wrapping other tools and putting them up on
Thanks Dannon for adding the Phylogenetics category,
I changed the name of this thread, to go in a related by new direction:
I wonder if the Galaxy developers and community have any opinions on
what is the best way to organize tools into repositories. We've
developed a large number of tools to
If I downloaded with curl -i, the page it returned was:
pwbcad@gamma01:tmp$ curl -i
http://galaxy-qa.garvan.unsw.edu.au/datasets/dc097fa4e7ad53f6/display?to_ext=fastqsanger
HTTP/1.1 302 Found
Date: Tue, 30 Oct 2012 04:25:21 GMT
Server: PasteWSGIServer/0.5 Python/2.6.6
content-type: text/html
locat
Hi Ross,
Good point and it makes sense in term of security. But I just tried it, and
it didn't help.
I captured these two from the Paste log (not apache log):
xx.xx.1xx.xx - - [30/Oct/2012:15:42:17 +1100] "GET
/galaxy_dev/datasets/10b866a1b258d1f1/display?to_ext=fastqsanger HTTP/1.1"
302 - "-" "
On Tue, Oct 30, 2012 at 4:03 PM, Ross wrote:
> Doesn't make sense that you can wget directly from the paste process
> if you have security properly configured!
>
That's what you can do with the main Galaxy site. Not sure if that's
intentional though. You can try
wget --no-check-certificate
http
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